Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016472.1 Corchorus olitorius cultivar O-4 contig16505, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 94532
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1270 original size:320 final size:314
Alignment explanation
Indices: 41--1505 Score: 1435
Period size: 318 Copynumber: 4.6 Consensus size: 314
31 AAAGTAGATT
* * *
41 TAAGGATTTATTTTCACGAGCATCTGAATCTTGATTCTATTTAATTAGAAATTAAATTC-AAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTTATTCTATTTAATTAGAAATT-AATTCGAAAAA
* * * * *
105 AAAAGGACAAACGATATTACAAGCTTCAAAATCCCGTCAATCTTTTTGGCATTGAATTTTA-AAA
65 AAAAGGAAAAACGATATTACAAACTTGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATAAA
* * * *
169 TTTTCTGAGTATTGTGACGAAAAAATTCGCAAAAAAAAAATTTGG-TCA-GTATTTAGCCGAAAT
130 TTTTCTGAGTATTGTGGC-AAAAATTTCG-GAAAAAAAAA-TCGGATCAGGT-TTTAGCCGAAAT
* *
232 CGTGTACACCATCATGATTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGAT
191 C--GT--A-CATCACGGTTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGAT
* * **
297 TTTTGGCAGAAATACTCCTTGAAATATCAATATTCATCTAACCAAAAGTCAGCCGCATTGGATA
251 TTTCGGCAGAAATACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATTGGATA
* *
361 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGT-TTTTATTTAATTAAAAATTAATTC--AAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTT-TATTCTATTTAATTAGAAATTAATTCGAAAAA
* * * * * * * * ** **
423 AAATGGAAAAACAATATTAGAAGCGTGAAAAACCTGCCAATCTTTTTGGCGTTGGGTTATATATT
65 AAAAGGAAAAACGATATTACAAACTTGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATAAA
* * *** *
488 TTTTCTGAGTATTGTTGCAAAAATTTCACGAAAAAATTTTCGGATCAGTTTTTAGCCG-AA-C--
130 TTTTCTGAGTATTGTGGCAAAAATTTC-GGAAAAAAAAATCGGATCAGGTTTTAGCCGAAATCGT
* * * *
549 -CATCACGGTTTTTTGGTTAAAAACGCGTTTCGGGACCTCGGCTCAGTTTTGCATGATTTTTGGC
194 ACATCACGG-TTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTCGGC
* *
613 AGAAA-ATCTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCCGCATTGGATA
258 AGAAATA-CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATTGGATA
*
670 TAAGTATTTGTTTTTACGAGCATCATCTGAATCTTGT-TTCTATTTAATTAGAAATTAATTCGAA
1 TAAGGATTTGTTTTTACGAG---CATCTGAATCTT-TATTCTATTTAATTAGAAATTAATTCGAA
** * * * ** * * *
734 AAAAATTGGAAAAACGATATTA-GAAGTGAGAAAAACATGTCGATCTTTTTCGCGTTGAATTATA
62 AAAAAAAGGAAAAACGATATTACAAACT-TGAAAAACCCGTCAATCTTTTTGGCATTGAATTATA
** * * *** * *
798 TATTTTTTCTGAGTATTGTTGCAAAAATTTTAC-GAAAGAATTTTCGGATCAGTTTTTAGCTGAA
126 TAAATTTTCTGAGTATTGTGGCAAAAA-TTT-CGGAAAAAAAAATCGGATCAGGTTTTAGCCGAA
* * * * *
862 ATCATACATCACGG-TTTTGACTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTT
189 ATCGTACATCACGGTTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTT
* * * * * * ** * *
926 CGGCAGAAAGATTCCTTAAAATATCTATATCCATATAACCAAGTCTCAGCCAAATTAGATT
254 CGGCAGAAATACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATTGGATA
*
987 TAAGGATTTATTTTTACGAGCATCTGAATCTTTATTCTATTTAATTAGAAATTAATTCGGAAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTTATTCTATTTAATTAGAAATTAATTC-G----A
* * *
1052 AAAAAAAAGGAAAAACGATATCACAAACTTGAAAATCCCGTCAATCTTTTTGACATTGAATTATA
61 AAAAAAAAGGAAAAACGATATTACAAACTTGAAAAACCCGTCAATCTTTTTGGCATTGAATTATA
*
1117 -AAATTTTCT-ACGTATTGTGGCGAAGAAA-TTCGGAAAAAAAAATCGG-TCAGGTTTTAGGCGA
126 TAAATTTTCTGA-GTATTGTGGC-AA-AAATTTCGGAAAAAAAAATCGGATCAGGTTTTAGCCGA
* * *
1178 AATCGTGTACGTCACGGTTTATGGCTAAAAACACGTTTCGGGGCCTCGACTCAGTTTTGCATGAT
188 AATC--GTACATCACGGTTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGAT
* * *
1243 TTTCGGCAGAAATACTCCTTGAAATATCGATATTTATCTAACCAAAAACTCAGCCGCATTGGATA
251 TTTCGGCAGAAATACTCCTTGAAATATCTATATTCATCTAACC-AAATCTCAGCCGCATTGGATA
* * * *
1308 CAAGGAATTGTTTTTACAAGCATCTGAATC-TTATTTCTATTTAATTAAAAATTAATTCGGAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTTA-TTCTATTTAATTAGAAATTAATTC-GAAAA
* * * * * * * * *
1372 AAAAATGGAAAAACAATATTAGAAGCGTGAAAAAACGGTCAATCTTTTTGACGTTGAGTTATATA
64 AAAAA-GGAAAAACGATATTACAAACTTGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATA
** * * ** * **
1437 TTTTTTCTGAGTATTGTTGCAAAAATTTCACGAAAAAAATTTTCGAATCAATTTTTAGCCGAAAT
128 AATTTTCTGAGTATTGTGGCAAAAATTTC-GGAAAAAAA-AATCGGATCAGGTTTTAGCCGAAAT
1502 CGTA
191 CGTA
1506 TACTAACTAT
Statistics
Matches: 955, Mismatches: 146, Indels: 89
0.80 0.12 0.07
Matches are distributed among these distances:
308 7 0.01
309 121 0.13
312 36 0.04
313 2 0.00
314 140 0.15
315 6 0.01
316 3 0.00
317 145 0.15
318 158 0.17
319 118 0.12
320 137 0.14
321 82 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (314 bp):
TAAGGATTTGTTTTTACGAGCATCTGAATCTTTATTCTATTTAATTAGAAATTAATTCGAAAAAA
AAAGGAAAAACGATATTACAAACTTGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATAAAT
TTTCTGAGTATTGTGGCAAAAATTTCGGAAAAAAAAATCGGATCAGGTTTTAGCCGAAATCGTAC
ATCACGGTTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTCGGCAGA
AATACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATTGGATA
Found at i:1442 original size:637 final size:626
Alignment explanation
Indices: 59--1502 Score: 1535
Period size: 637 Copynumber: 2.3 Consensus size: 626
49 TATTTTCACG
* * * *
59 AGCATCTGAATCTTGA-TTCTATTTAATTAGAAATTAAATTC-AAAAAAAAAGGACAAACGATAT
1 AGCATCTGAATCTT-ATTTCTATTTAATTAAAAATT-AATTCGAAAAAAAATGGAAAAACAATAT
* ** * ** * * * **
122 TACAAGCT-TCAAAATCCCGTCAATCTTTTTGGCATTGAATTTTA-AAATTTTCTGAGTATTG-T
64 TAGAAG-TGAGAAAAACAGGTCAATCTTTTTCGCGTTGAATTATATATTTTTTCTGAGTATTGTT
* * * * * * * * *
184 GACGAAAAAATTCGCAAAAAAAAAATTT-G-GTCAGTATTTAGCCGAAATCGTGTACACCATCAT
128 G-C-AAAAATTTCAC-GAAAAAAATTTTCGAATCAATTTTTAGCCGAAATC----ATA-CATCAC
* * * * * *
247 GATTTTTGGCTAAAAACACGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCAGAAATAC
185 G-GTTTTGACTAAAAACACGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGAAAGAC
* * * * ** * *
312 TCCTTGAAATATCAATATTCATCTAACCAAAAGTCAGCCGCATTGGATATAAGGATTTGTTTTTA
249 TCCTTAAAATATCAATATCCATATAACCAAAACTCAGCCAAATTAGATATAAGGATTTATTTTTA
* * *
377 CGAGCATCTGAATCTTGTTTTTATTTAATTAAAAATTAATTCAAAAAAATGGAAAAACAATATTA
314 CGAGCATCTGAATCTTGTTTCTATTTAATTAAAAATTAATTCAAAAAAAAGGAAAAACAATATCA
* * * * * ** ** *
442 GAAGCGTGAAAAACCTGCCAATCTTTTTGGCGTTGGGTTATATATTTTTTCTGAGTATTGTTGCA
379 CAAACGTGAAAAACCCGCCAATCTTTTTGACATTGAATTATATAAATTTTCTGAGTATTGTGGCA
*** * * *
507 AAAATTTCACGAAAAAATTTTCGGATCAGTTTTTAGCCGAACCATCACGGTTTTTTGGTTAAAAA
444 AAAATTTCACGAAAAAAAAATCGGATCAGGTTTTAGCCGAACCATCACGGTTTTATGGCTAAAAA
* * * **
572 CGCGTTTCGGGACCTCGGCTCAGTTTTGCATGATTTTTGGCAGAAAATCTCCTTGAAATATTTAT
509 CACGTTTCGGGACCTCGACTCAGTTTTGCATGATTTTCGGCAGAAAATCTCCTTGAAATATCGAT
* * * * *
637 ATTCATCTAATCAAATCTCAGCCGCATTGGATATAAGTATTTGTTTTTACGAGC
574 ATTCATCTAACCAAAACTCAGCCGCATTGGATACAAGGAATTGTTTTTACGA-C
* * * * *
691 ATCATCTGAATCTTGTTTCTATTTAATTAGAAATTAATTCGAAAAAAATTGGAAAAACGATATTA
1 AGCATCTGAATCTTATTTCTATTTAATTAAAAATTAATTCGAAAAAAAATGGAAAAACAATATTA
* *
756 GAAGTGAGAAAAACATGTCGATCTTTTTCGCGTTGAATTATATATTTTTTCTGAGTATTGTTGCA
66 GAAGTGAGAAAAACAGGTCAATCTTTTTCGCGTTGAATTATATATTTTTTCTGAGTATTGTTGCA
* * * * *
821 AAAATTTTACG-AAAGAATTTTCGGATCAGTTTTTAGCTGAAATCATACATCACGGTTTTGACTA
131 AAAATTTCACGAAAAAAATTTTCGAATCAATTTTTAGCCGAAATCATACATCACGGTTTTGACTA
* *
885 AAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGAAAGATTCCTTAAAATAT
196 AAAACACGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGAAAGACTCCTTAAAATAT
* ** *
950 CTATATCCATATAACCAAGTCTCAGCCAAATTAGATTTAAGGATTTATTTTTACGAGCATCTGAA
261 CAATATCCATATAACCAAAACTCAGCCAAATTAGATATAAGGATTTATTTTTACGAGCATCTGAA
* *
1015 TCTT-TATTCTATTTAATTAGAAATTAATTCGGAAAAAAAAAAAAAGGAAAAACGATATCACAAA
326 TCTTGT-TTCTATTTAATTAAAAATTAATTC-------AAAAAAAAGGAAAAACAATATCACAAA
* * *
1079 CTTGAAAATCCCGTCAATCTTTTTGACATTGAATTATA-AAATTTTCT-ACGTATTGTGGCGAAG
383 CGTGAAAAACCCGCCAATCTTTTTGACATTGAATTATATAAATTTTCTGA-GTATTGTGGC-AA-
* * *
1142 AAA-TTC-GGAAAAAAAAATCGG-TCAGGTTTTAGGCGAAATCGTGTACGTCACGG-TTTATGGC
445 AAATTTCACGAAAAAAAAATCGGATCAGGTTTTAGCCG-AA-C-----CATCACGGTTTTATGGC
*
1203 TAAAAACACGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTCGGCAG-AAATACTCCTTGAAA
503 TAAAAACACGTTTCGGGACCTCGACTCAGTTTTGCATGATTTTCGGCAGAAAAT-CTCCTTGAAA
*
1267 TATCGATATTTATCTAACCAAAAACTCAGCCGCATTGGATACAAGGAATTGTTTTTAC-A-
567 TATCGATATTCATCTAACC-AAAACTCAGCCGCATTGGATACAAGGAATTGTTTTTACGAC
1326 AGCATCTGAATCTTATTTCTATTTAATTAAAAATTAATTCGGAAAAAAAAATGGAAAAACAATAT
1 AGCATCTGAATCTTATTTCTATTTAATTAAAAATTAATTC-G-AAAAAAAATGGAAAAACAATAT
*
1391 TAGAAGCGTGA-AAAAAC-GGTCAATCTTTTT-GACGTTGAGTTATATATTTTTTCTGAGTATTG
64 TAGAA--GTGAGAAAAACAGGTCAATCTTTTTCG-CGTTGAATTATATATTTTTTCTGAGTATTG
1453 TTGCAAAAATTTCACGAAAAAAATTTTCGAATCAATTTTTAGCCGAAATC
126 TTGCAAAAATTTCACGAAAAAAATTTTCGAATCAATTTTTAGCCGAAATC
1503 GTATACTAAC
Statistics
Matches: 679, Mismatches: 100, Indels: 60
0.81 0.12 0.07
Matches are distributed among these distances:
625 1 0.00
626 146 0.22
627 6 0.01
628 2 0.00
630 8 0.01
631 20 0.03
632 137 0.20
633 74 0.11
634 5 0.01
635 37 0.05
636 6 0.01
637 157 0.23
638 76 0.11
639 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (626 bp):
AGCATCTGAATCTTATTTCTATTTAATTAAAAATTAATTCGAAAAAAAATGGAAAAACAATATTA
GAAGTGAGAAAAACAGGTCAATCTTTTTCGCGTTGAATTATATATTTTTTCTGAGTATTGTTGCA
AAAATTTCACGAAAAAAATTTTCGAATCAATTTTTAGCCGAAATCATACATCACGGTTTTGACTA
AAAACACGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGAAAGACTCCTTAAAATAT
CAATATCCATATAACCAAAACTCAGCCAAATTAGATATAAGGATTTATTTTTACGAGCATCTGAA
TCTTGTTTCTATTTAATTAAAAATTAATTCAAAAAAAAGGAAAAACAATATCACAAACGTGAAAA
ACCCGCCAATCTTTTTGACATTGAATTATATAAATTTTCTGAGTATTGTGGCAAAAATTTCACGA
AAAAAAAATCGGATCAGGTTTTAGCCGAACCATCACGGTTTTATGGCTAAAAACACGTTTCGGGA
CCTCGACTCAGTTTTGCATGATTTTCGGCAGAAAATCTCCTTGAAATATCGATATTCATCTAACC
AAAACTCAGCCGCATTGGATACAAGGAATTGTTTTTACGAC
Found at i:6107 original size:72 final size:72
Alignment explanation
Indices: 5981--6146 Score: 226
Period size: 72 Copynumber: 2.3 Consensus size: 72
5971 TTCTTTGAAT
* * * * *
5981 AGTTTGCTTAAAGTGTGTAAAGGCATTGCCTTTCGTTGAGTTTTACATGTTTCTGTGGTGTTATC
1 AGTTTACTAAAAGTGTGTAAAGGCATTGCCTTTCATTGAGTTTTACATGCTTCTGTGGTGTAATC
**
6046 TTTTTGA
66 TTTTCCA
* * *
6053 AGTTTACTAAAAGTGTGTAAAGGCTTTGCCTTTCATTG-GTTTTTGCTTGCTTCTGTGGTGTAAT
1 AGTTTACTAAAAGTGTGTAAAGGCATTGCCTTTCATTGAG-TTTTACATGCTTCTGTGGTGTAAT
6117 CTTTTCCA
65 CTTTTCCA
6125 AGTTTACTAAAAGTGTGTAAAG
1 AGTTTACTAAAAGTGTGTAAAG
6147 TCTTAATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
71 1 0.01
72 82 0.99
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (72 bp):
AGTTTACTAAAAGTGTGTAAAGGCATTGCCTTTCATTGAGTTTTACATGCTTCTGTGGTGTAATC
TTTTCCA
Found at i:12711 original size:18 final size:18
Alignment explanation
Indices: 12690--12726 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12680 ATTGAACTTG
*
12690 ACATATAATTGGGCCTTC
1 ACATAGAATTGGGCCTTC
*
12708 ACATAGGATTGGGCCTTC
1 ACATAGAATTGGGCCTTC
12726 A
1 A
12727 TTTCATACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (18 bp):
ACATAGAATTGGGCCTTC
Found at i:20080 original size:2 final size:2
Alignment explanation
Indices: 20073--20114 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20063 CTTTGAAGAA
20073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20115 CAACAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23144 original size:32 final size:31
Alignment explanation
Indices: 23074--23144 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
23064 TTTAAATCAC
* *
23074 GACAATTTGTCTCATGAATTCCCAAATTCAG
1 GACAATTTGTCTCATGAATTCCCAAATCCAA
* *
23105 GATAATTTGCTCTCA-GAACTTCTCAAATCCAA
1 GACAATTTG-TCTCATGAA-TTCCCAAATCCAA
23137 GACAATTT
1 GACAATTT
23145 ACCTCTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 11 0.33
32 22 0.67
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (31 bp):
GACAATTTGTCTCATGAATTCCCAAATCCAA
Found at i:23834 original size:33 final size:33
Alignment explanation
Indices: 23791--23862 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
23781 TTGAAGATTT
* *
23791 TGTATTCTTGCATTTGAGTATTACGTATATGGA
1 TGTATACTTGCATTTGAGTAGTACGTATATGGA
23824 TGTATACTTGCATTTGAGTAGTACGTATATGGA
1 TGTATACTTGCATTTGAGTAGTACGTATATGGA
23857 TGTATA
1 TGTATA
23863 TGAATACGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (33 bp):
TGTATACTTGCATTTGAGTAGTACGTATATGGA
Found at i:32388 original size:121 final size:123
Alignment explanation
Indices: 32237--32479 Score: 373
Period size: 124 Copynumber: 2.0 Consensus size: 123
32227 AGTTATAGTC
* *
32237 GTTTCTTGAGTAGGTACGCATAAGGGAAATCATATTTTAGAACTT-C-GGACTTTGTTTTGGAAT
1 GTTTCTTGAGTAGGGACGCATAAGGAAAATCATATTTTAGAACTTACGGGACTTTGTTTTGGAAT
*
32300 TTCAGAATATGATAGTTTGGTAAAATGATTATTAATTAATGATCTTAACTAAATGATT
66 TTCAGAATATGATAGTTCGGTAAAATGATTATTAATTAATGATCTTAACTAAATGATT
* * **
32358 GTTTCTTGAGTAGGGATGCGTAAGGAAAATCATATTTTAGAACTTAACGGGGTTTTGTTTTGGAA
1 GTTTCTTGAGTAGGGACGCATAAGGAAAATCATATTTTAGAACTT-ACGGGACTTTGTTTTGGAA
* * *
32423 TTTCAGAGTATGATAGTTCGGTAAGATGATTATTAATTAATGATCTTAATTAAATGA
65 TTTCAGAATATGATAGTTCGGTAAAATGATTATTAATTAATGATCTTAACTAAATGA
32480 AATCAAATCG
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
121 41 0.38
123 1 0.01
124 67 0.61
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (123 bp):
GTTTCTTGAGTAGGGACGCATAAGGAAAATCATATTTTAGAACTTACGGGACTTTGTTTTGGAAT
TTCAGAATATGATAGTTCGGTAAAATGATTATTAATTAATGATCTTAACTAAATGATT
Found at i:43938 original size:55 final size:55
Alignment explanation
Indices: 43854--43963 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
43844 AGCTCTAGAT
43854 ATTGAAAGTGGAGGAAACTAATCAATTTTTTGACACCCACGAAAAGACTCCAAAC
1 ATTGAAAGTGGAGGAAACTAATCAATTTTTTGACACCCACGAAAAGACTCCAAAC
43909 ATTGAAAGTGGAGGAAACTAATCAATTTTTTGACACCCACGAAAAGACTCCAAAC
1 ATTGAAAGTGGAGGAAACTAATCAATTTTTTGACACCCACGAAAAGACTCCAAAC
43964 GTATTAGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (55 bp):
ATTGAAAGTGGAGGAAACTAATCAATTTTTTGACACCCACGAAAAGACTCCAAAC
Found at i:54779 original size:41 final size:41
Alignment explanation
Indices: 54726--54808 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
54716 ATGCCATTAA
* *
54726 ATAAATTTAATAAAGAAATCATATAATATAACCGGTAAAAT
1 ATAAATTTAATAAAGAAATCAGATAATATAACCGGAAAAAT
*
54767 ATAAATTTAATAAAGAAATCAGATAATATAATCGGAAAAAT
1 ATAAATTTAATAAAGAAATCAGATAATATAACCGGAAAAAT
54808 A
1 A
54809 ACGGGAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (41 bp):
ATAAATTTAATAAAGAAATCAGATAATATAACCGGAAAAAT
Found at i:75217 original size:27 final size:27
Alignment explanation
Indices: 75179--75233 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
75169 GGAATGCTGA
75179 TATCGGGGAAAACAACACCAAACCATC
1 TATCGGGGAAAACAACACCAAACCATC
75206 TATCGGGGAAAACAACACCAAACCATC
1 TATCGGGGAAAACAACACCAAACCATC
75233 T
1 T
75234 TTGTTACGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.29, G:0.15, T:0.13
Consensus pattern (27 bp):
TATCGGGGAAAACAACACCAAACCATC
Found at i:78474 original size:19 final size:19
Alignment explanation
Indices: 78450--78486 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
78440 CTGTTTAATA
*
78450 ACTGTACAGATGAGATTAC
1 ACTGTACAAATGAGATTAC
78469 ACTGTACAAATGAGATTA
1 ACTGTACAAATGAGATTA
78487 TTAGAGCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAC
Found at i:88936 original size:24 final size:25
Alignment explanation
Indices: 88904--88954 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
88894 AGACACACAA
* *
88904 AACCTTCGGC-CAAAAAACAGACAT
1 AACCTTCGGCAAAAAAAAAAGACAT
88928 AACCTTCGGCAAAAAAAAAAGACAT
1 AACCTTCGGCAAAAAAAAAAGACAT
88953 AA
1 AA
88955 AACCTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (25 bp):
AACCTTCGGCAAAAAAAAAAGACAT
Found at i:89581 original size:31 final size:31
Alignment explanation
Indices: 89543--89683 Score: 192
Period size: 31 Copynumber: 4.5 Consensus size: 31
89533 ACGGTGTCCA
* *
89543 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
*
89574 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
***
89605 ACGTGGCATGCCACGTGTTTTAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* **
89636 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
*
89667 ACATGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
89684 CACAAAAGGA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:92252 original size:51 final size:51
Alignment explanation
Indices: 92169--92323 Score: 256
Period size: 51 Copynumber: 3.0 Consensus size: 51
92159 TAAAAAATAT
* * *
92169 GACAACTCATCATAGTCAATTGCCAAATGAAATTTGCAAGGAAATCTTAGA
1 GACAACTCATCATAGTCAATTGCCAGAGGAAATTTGCATGGAAATCTTAGA
** *
92220 GACAACTCATCATAGTCAATTTTCAGAGGAAATTTGCATGGAAATTTTAGA
1 GACAACTCATCATAGTCAATTGCCAGAGGAAATTTGCATGGAAATCTTAGA
92271 GACAACTCATCATAGTCAATTGCCAGAGGAAATTTGCATGGAAATCTTAGA
1 GACAACTCATCATAGTCAATTGCCAGAGGAAATTTGCATGGAAATCTTAGA
92322 GA
1 GA
92324 AATTACCTAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 95 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (51 bp):
GACAACTCATCATAGTCAATTGCCAGAGGAAATTTGCATGGAAATCTTAGA
Done.